We propose a (recursive) DNA algorithm for adding two binary numbers which require O(log n) bio-steps using only O(n) different type of DNA strands, where n is the size of the binary string representing the larger of the two numbers. The salient feature of our technique is that the input strands and the output strands have exactly the same structure which makes it fully procedural unlike most m...

One of the important factors influencing outdoor insulators performance is pollution phenomenon. The pollution, especially during humidity condition, reduces superficial resistance of insulator and lead to a flow of Leakage Currents (LC) on the insulator surface, which may result in total flashover. The LC characteristics are affected by parameters such as nature and severity of pollution. Loca...

The DNA fragment assembly is an essential step in DNA sequencing projects. Since DNA sequencers output fragments, the original genome must be reconstructed from these small reads. In this paper, a new fragment assembly algorithm, Pattern Matching based String Graph Assembler (PMSGA), is presented. The algorithm uses multipattern matching to detect overlaps and a minimum cost flow algorithm to d...

Of late Molecular biology is becoming increasingly dependent on computer science algorithms as research tools. The process of aligning DNA sequences is widely used in modern biological sciences. Genetics databases hold extremely large amount of raw data. The human genome alone has approximately 3 billion DNA base pairs. To search through all this data and to find meaningful relationships in it,...

In most metazoans, early embryonic development is characterized by rapid mitotic divisions that are controlled by maternal mRNAs and proteins that accumulate during oogenesis. These rapid divisions pause at the midblastula transition (MBT), coinciding with a dramatic increase in gene transcription and the degradation of a subset of maternal mRNAs. In Drosophila, the cell-cycle pause is controll...

We performed molecular dynamics simulations of the genome packaging of bacteriophage P4 using two coarse-grained models of DNA. The first model, 1DNA6 (one pseudo-atom per six DNA basepairs), represents DNA as a string of beads, for which DNA torsions are undefined. The second model, 3DNA6 (three pseudo-atoms per six DNA basepairs), represents DNA as a series of base planes with torsions define...

Self-assembly creates natural mineral, chemical, and biological structures of great complexity. Often, the same starting materials have the potential to form an infinite variety of distinct structures; information in a seed molecule can determine which form is grown as well as where and when. These phenomena can be exploited to program the growth of complex supramolecular structures, as demonst...

Through sequence-based classification, this paper tries to accurately predict the DNA binding sites of transcription factors (TFs) in an unannotated cellular context. Related methods in the literature fail to perform such predictions accurately, since they do not consider sample distribution shift of sequence segments from an annotated (source) context to an unannotated (target) context. We, th...

Approximate string matching is a fundamental and challenging problem in computer science, for which a fast algorithm is highly demanded in many applications including text processing and DNA sequence analysis. In this paper, we present a fast algorithm for approximate string matching, called FAAST. It aims at solving a popular variant of the approximate string matching problem, the k-mismatch p...

We consider the problem of on-line exact string matching of a pattern in a set of highly similar sequences. This can be useful in cases where indexing the sequences is not feasible. We present a preliminary study by restricting the problem for a specific case where we adapt the classical Morris-Pratt algorithm to consider borders with errors. We give an original algorithm for computing borders ...